Contacts of the strand formed by residues 228 - 235 (chain Q) in PDB entry 3K9Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 228 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156Q LEU* 4.4 14.8 - - + -
160Q ALA* 4.0 15.9 - - + -
169Q LEU* 3.9 20.4 - - + -
172Q GLY* 3.5 25.6 - - - +
214Q ALA* 3.3 30.3 + - + +
215Q LYS* 3.6 8.0 - - - +
217Q ILE* 3.8 24.8 - - + +
224Q ILE* 4.0 15.3 + - + -
226Q GLY* 4.5 3.7 - - - +
227Q LYS* 1.3 90.0 + - - +
229Q ASP* 1.3 65.3 + - - +
245Q LEU* 3.9 17.0 - - + -
247Q VAL* 4.5 1.3 - - + -
300R MET* 3.3 6.1 - - - +
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Residues in contact with ASP 229 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172Q GLY 3.4 5.1 + - - -
173Q LEU* 3.3 14.3 - - + -
174Q MET* 2.8 25.5 + - - +
211Q THR 5.1 1.0 - - - +
214Q ALA* 3.5 12.3 - - - -
215Q LYS* 3.4 43.1 + - - +
228Q LEU* 1.3 75.7 - - - +
230Q GLY* 1.3 77.5 + - - +
298R ARG* 3.0 30.5 + - + +
299R VAL 5.7 0.5 - - - +
300R MET* 3.5 16.1 - - + +
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Residues in contact with GLY 230 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173Q LEU* 4.5 0.2 - - - -
174Q MET* 3.1 21.7 - - - +
211Q THR 3.7 15.2 + - - +
214Q ALA* 4.1 0.9 - - - +
229Q ASP* 1.3 95.5 + - - +
231Q GLY* 1.3 58.5 + - - -
298R ARG* 3.5 28.1 + - - +
309R LYS* 4.5 2.2 - - - -
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Residues in contact with GLY 231 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174Q MET* 3.2 10.0 + - - +
175Q THR* 3.5 7.1 + - - -
176Q THR* 3.1 25.1 + - - +
209Q ASN 3.8 6.3 - - - -
211Q THR* 3.7 14.4 - - - -
230Q GLY* 1.3 74.3 - - - -
232Q ALA* 1.3 60.9 + - - -
298R ARG* 4.3 9.9 - - - +
309R LYS* 4.7 2.4 - - - +
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Residues in contact with ALA 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q THR* 4.9 1.1 - - - -
176Q THR* 3.3 22.7 - - + +
178Q HIS* 4.9 7.4 - - + -
208Q PRO* 3.4 5.2 - - - +
209Q ASN* 2.8 43.5 + - + +
210Q SER 4.5 3.1 - - - +
211Q THR* 4.1 9.0 - - + -
231Q GLY* 1.3 75.0 - - - +
233Q GLN* 1.3 72.2 + - - +
234Q ARG* 4.9 7.4 - - - +
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Residues in contact with GLN 233 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q THR* 4.1 16.1 - - + +
176Q THR 2.9 7.7 + - - +
177Q ILE* 3.5 5.9 - - - -
178Q HIS 2.8 24.3 + - - -
206Q ILE* 3.8 16.5 - - + +
207Q ILE 3.5 1.1 - - - -
208Q PRO* 3.1 29.7 - - - +
232Q ALA* 1.3 81.2 + - - +
234Q ARG* 1.3 61.9 + - - +
235Q VAL* 3.6 6.8 + - + +
177R ILE* 4.2 16.4 - - + -
242R LEU* 3.2 23.6 - - - +
244R GLU* 2.8 24.7 + - - +
296R GLN* 3.3 14.1 - - - +
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Residues in contact with ARG 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Q HIS* 3.2 29.0 + - - +
179Q ALA 3.6 15.0 - - - -
180Q TYR* 4.8 2.0 - - - -
181Q THR* 2.9 26.9 + - - +
183Q ASP* 3.5 14.3 + - - -
184Q GLN* 2.7 52.6 + - - +
198Q ARG* 4.9 4.5 - - + +
202Q ALA 5.7 0.4 - - - -
205Q ASN 3.4 5.8 - - - +
207Q ILE* 2.8 46.5 + - + +
209Q ASN* 4.4 20.4 + - + +
232Q ALA* 4.9 7.7 - - + +
233Q GLN* 1.3 70.9 - - - +
235Q VAL* 1.3 59.2 + - - +
337Q GOL 4.2 22.6 - - - -
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Residues in contact with VAL 235 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177Q ILE* 3.7 33.9 - - + -
178Q HIS 2.9 13.1 + - - +
179Q ALA* 4.0 0.2 - - - -
180Q TYR* 3.5 19.3 + - - +
202Q ALA 4.7 1.8 - - - -
205Q ASN 3.9 0.9 - - - -
206Q ILE* 4.3 9.2 - - + -
233Q GLN 3.9 6.5 - - - +
234Q ARG* 1.3 77.5 - - - +
236Q PRO* 1.3 70.7 - - + +
237Q VAL* 2.8 14.3 + - + +
177R ILE* 4.2 9.2 - - + -
206R ILE* 3.8 23.1 - - + -
235R VAL* 4.0 25.4 - - + -
236R PRO* 4.8 1.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il